diff --git a/rhodecode/lib/utils.py b/rhodecode/lib/utils.py
--- a/rhodecode/lib/utils.py
+++ b/rhodecode/lib/utils.py
@@ -467,9 +467,9 @@ def repo2db_mapper(initial_repo_list, re
                 log.debug("Removing non-existing repository found in db `%s`" %
                           repo.repo_name)
                 try:
-                    sa.delete(repo)
+                    removed.append(repo.repo_name)
+                    RepoModel(sa).delete(repo, forks='detach', fs_remove=False)
                     sa.commit()
-                    removed.append(repo.repo_name)
                 except Exception:
                     #don't hold further removals on error
                     log.error(traceback.format_exc())